- Award ID(s):
- 1815674
- NSF-PAR ID:
- 10185931
- Date Published:
- Journal Name:
- Bioinformatics
- ISSN:
- 1367-4803
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)Learning the low-dimensional representations of graphs (i.e., network embedding) plays a critical role in network analysis and facilitates many downstream tasks. Recently graph convolutional networks (GCNs) have revolutionized the field of network embedding, and led to state-of-the-art performance in network analysis tasks such as link prediction and node classification. Nevertheless, most of the existing GCN-based network embedding methods are proposed for unsigned networks. However, in the real world, some of the networks are signed, where the links are annotated with different polarities, e.g., positive vs. negative. Since negative links may have different properties from the positive ones and can also significantly affect the quality of network embedding. Thus in this paper, we propose a novel network embedding framework SNEA to learn Signed Network Embedding via graph Attention. In particular, we propose a masked self-attentional layer, which leverages self-attention mechanism to estimate the importance coefficient for pair of nodes connected by different type of links during the embedding aggregation process. Then SNEA utilizes the masked self-attentional layers to aggregate more important information from neighboring nodes to generate the node embeddings based on balance theory. Experimental results demonstrate the effectiveness of the proposed framework through signed link prediction task on several real-world signed network datasets.more » « less
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Abstract Motivation Accurately predicting drug–target interactions (DTIs) in silico can guide the drug discovery process and thus facilitate drug development. Computational approaches for DTI prediction that adopt the systems biology perspective generally exploit the rationale that the properties of drugs and targets can be characterized by their functional roles in biological networks.
Results Inspired by recent advance of information passing and aggregation techniques that generalize the convolution neural networks to mine large-scale graph data and greatly improve the performance of many network-related prediction tasks, we develop a new nonlinear end-to-end learning model, called NeoDTI, that integrates diverse information from heterogeneous network data and automatically learns topology-preserving representations of drugs and targets to facilitate DTI prediction. The substantial prediction performance improvement over other state-of-the-art DTI prediction methods as well as several novel predicted DTIs with evidence supports from previous studies have demonstrated the superior predictive power of NeoDTI. In addition, NeoDTI is robust against a wide range of choices of hyperparameters and is ready to integrate more drug and target related information (e.g. compound–protein binding affinity data). All these results suggest that NeoDTI can offer a powerful and robust tool for drug development and drug repositioning.
Availability and implementation The source code and data used in NeoDTI are available at: https://github.com/FangpingWan/NeoDTI.
Supplementary information Supplementary data are available at Bioinformatics online.
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Abstract Noncoding RNAs (ncRNAs) have recently attracted considerable attention due to their key roles in biology. The ncRNA–proteins interaction (NPI) is often explored to reveal some biological activities that ncRNA may affect, such as biological traits, diseases, etc. Traditional experimental methods can accomplish this work but are often labor-intensive and expensive. Machine learning and deep learning methods have achieved great success by exploiting sufficient sequence or structure information. Graph Neural Network (GNN)-based methods consider the topology in ncRNA–protein graphs and perform well on tasks like NPI prediction. Based on GNN, some pairwise constraint methods have been developed to apply on homogeneous networks, but not used for NPI prediction on heterogeneous networks. In this paper, we construct a pairwise constrained NPI predictor based on dual Graph Convolutional Network (GCN) called NPI-DGCN. To our knowledge, our method is the first to train a heterogeneous graph-based model using a pairwise learning strategy. Instead of binary classification, we use a rank layer to calculate the score of an ncRNA–protein pair. Moreover, our model is the first to predict NPIs on the ncRNA–protein bipartite graph rather than the homogeneous graph. We transform the original ncRNA–protein bipartite graph into two homogenous graphs on which to explore second-order implicit relationships. At the same time, we model direct interactions between two homogenous graphs to explore explicit relationships. Experimental results on the four standard datasets indicate that our method achieves competitive performance with other state-of-the-art methods. And the model is available at https://github.com/zhuoninnin1992/NPIPredict
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